Sun Oct 9 14:39:01 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:39:01 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1373 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.8499057 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -9.937000 24.54200 ymin,ymax (A): -9.076000 30.65200 zmin,zma (A): -6.478000 35.40900 x,y,z range (A): 34.47900 39.72800 41.88700 scale (grids/A): 0.8499057 object centre (A): 7.302500 10.78800 14.46550 number of atom coordinates read : 1373 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 203.9293 centred at (gu) : 90.44019 88.66191 90.84328 assigned negative charge : -204.4291 centred at (gu) : 90.47967 88.76783 90.51894 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6772 nv = 96 ne = 84 npr = 29749 no. pairs analyzed = 29749 no. exposed pairs = 1707 no. arc points = 12500 no. surface atoms = 575 nbur = 798 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 608 mr = 3795 m= 10 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 5.9999995E-02 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.1300000 number of dielectric boundary points 3453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 810 ## 68 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 6337 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3969245E-06 1.5640293E-06 midg,1,midg; midg,igrid,midg 4.9409130E-07 -4.6044426E-07 1,midg,midg; igrid,midg,midg 8.4870280E-08 -2.8945465E-07 gauss-seidel spectral radius is 0.9926933 estimated iterations to convergence 95 setup time was (sec) 0.3100000 now iterating at: 14:39:01 rms-change max change #iterations 0.3284451 46.79771 at 10iterations 5.6397326E-02 6.909084 at 20iterations 9.8099187E-03 1.313019 at 30iterations 1.6643810E-03 0.2294722 at 40iterations 2.8962566E-04 3.9432526E-02 at 50iterations finished qdiffx linear iterations at : 14:39:04 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.8962566E-04 3.9432526E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 14:39:05 3.327u 0.186s 0:03.79 92.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:39:05 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1373 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.549717 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -9.937000 24.54200 ymin,ymax (A): -9.076000 30.65200 zmin,zma (A): -6.478000 35.40900 x,y,z range (A): 34.47900 39.72800 41.88700 scale (grids/A): 2.549717 object centre (A): 7.302500 10.78800 14.46550 number of atom coordinates read : 1373 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 203.9293 centred at (gu) : 91.32064 85.98603 92.53006 assigned negative charge : -204.4291 centred at (gu) : 91.43898 86.30354 91.55677 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12500 grid for indexing accessible points = 1.400000 m= 29553 mr = 47652 m= 7672 mr = 22885 m= 1267 mr = 5405 m= 153 mr = 749 m= 7 mr = 95 m= 0 mr = 4 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1182 time to turn everything in is 0.3800000 number of dielectric boundary points 31434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 10015 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.8499057 object centre at (A) : 7.302500 10.78800 14.46550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7425246E-02 9.1734491E-02 midg,1,midg; midg,igrid,midg 1.8538447E-02 -6.9823012E-02 1,midg,midg; igrid,midg,midg -1.3824757E-02 8.7998277E-03 gauss-seidel spectral radius is 0.9990711 estimated iterations to convergence 259 setup time was (sec) 0.6000000 now iterating at: 14:39:05 rms-change max change #iterations 4.985688 278.3744 at 10iterations 2.664612 106.3298 at 20iterations 1.422266 39.52267 at 30iterations 0.7598960 26.41644 at 40iterations 0.4071563 15.03595 at 50iterations 0.2179576 6.412512 at 60iterations 0.1164406 3.262024 at 70iterations 6.2348969E-02 1.950111 at 80iterations 3.3110872E-02 0.9293413 at 90iterations 1.7772926E-02 0.5263758 at 100iterations 9.4937775E-03 0.2906590 at 110iterations 5.0668861E-03 0.1361084 at 120iterations finished qdiffx linear iterations at : 14:39:12 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 5.0668861E-03 0.1361084 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 14:39:13 7.857u 0.197s 0:08.35 96.2% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sun Oct 9 2011 at 14:39:13 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1373 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.824576 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -9.937000 24.54200 ymin,ymax (A): -9.076000 30.65200 zmin,zma (A): -6.478000 35.40900 x,y,z range (A): 34.47900 39.72800 41.88700 scale (grids/A): 3.824576 object centre (A): 7.302500 10.78800 14.46550 number of atom coordinates read : 1373 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 203.9293 centred at (gu) : 91.98109 83.97890 93.79517 assigned negative charge : -204.4291 centred at (gu) : 92.15848 84.45534 92.33511 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 159762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12500 grid for indexing accessible points = 1.400000 m= 87575 mr = 114322 m= 41341 mr = 73303 m= 15464 mr = 34847 m= 4429 mr = 12341 m= 1175 mr = 3258 m= 235 mr = 914 m= 18 mr = 172 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 3973 time to turn everything in is 1.170000 number of dielectric boundary points 70829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 10020 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 2.549717 object centre at (A) : 7.302500 10.78800 14.46550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1079788 0.5236073 midg,1,midg; midg,igrid,midg 0.1460446 -0.5313374 1,midg,midg; igrid,midg,midg -0.1372425 0.1477813 gauss-seidel spectral radius is 0.9993379 estimated iterations to convergence 307 setup time was (sec) 1.410000 now iterating at: 14:39:15 rms-change max change #iterations 10.22407 273.2271 at 10iterations 6.064723 135.5128 at 20iterations 3.580972 65.04948 at 30iterations 2.116592 39.60148 at 40iterations 1.251285 22.92660 at 50iterations 0.7416100 12.31380 at 60iterations 0.4384788 7.082478 at 70iterations 0.2585892 4.804605 at 80iterations 0.1532032 2.526070 at 90iterations 9.0543464E-02 1.507221 at 100iterations 5.3706113E-02 1.076504 at 110iterations 3.1820200E-02 0.5756490 at 120iterations 1.8833036E-02 0.3438950 at 130iterations 1.1191856E-02 0.1922684 at 140iterations 6.7006145E-03 0.1083603 at 150iterations 4.0150895E-03 6.9526672E-02 at 160iterations 2.4411096E-03 4.2068481E-02 at 170iterations 1.5121397E-03 2.8266907E-02 at 180iterations finished qdiffx linear iterations at : 14:39:26 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 1.5121397E-03 2.8266907E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.92000 DelPhi exited at 14:39:26 12.923u 0.223s 0:13.42 97.9% 0+0k 0+0io 0pf+0w